stats: Fix of mismmatch-per-cycle calculation in presence of hard-clipped reads
Usage message tweaks to satisfy test/test.pl's test_usage()

Idxstats is currently disabled, but re-enable its basic functionality
including usage.  The calmd/fillmd command is canonically calmd.
Fix bamshuf and faidx messages.  Tview has been disabled in bamtk.c
for a while; also suppress it in samtools --help command listing.
Moved khash_utils.h into htslib
Updated the khash_utils.h dependency